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[DL-Learner SVN] SF.net SVN: dl-learner:[3891] trunk
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From: <lor...@us...> - 2013-01-25 12:02:22
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Revision: 3891
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3891&view=rev
Author: lorenz_b
Date: 2013-01-25 12:02:10 +0000 (Fri, 25 Jan 2013)
Log Message:
-----------
Started script for instance based matching of 2 SPARQL knowledge bases.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java
trunk/components-core/src/main/java/org/dllearner/learningproblems/PosOnlyLP.java
trunk/scripts/pom.xml
trunk/scripts/src/main/java/org/dllearner/scripts/matching/GeneralMatcher.java
trunk/test/qtl/dbpedia_simple.conf
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMatching.java
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java 2013-01-23 13:30:14 UTC (rev 3890)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java 2013-01-25 12:02:10 UTC (rev 3891)
@@ -701,7 +701,7 @@
public Set<NamedClass> getAllClasses() {
Set<NamedClass> classes = new TreeSet<NamedClass>();
- String query = "PREFIX owl: <http://www.w3.org/2002/07/owl#> SELECT ?c WHERE {?c a owl:Class} LIMIT 1000";
+ String query = "SELECT ?c WHERE {?c a <http://www.w3.org/2002/07/owl#Class>} LIMIT 1000";
/*
* String query = "PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> " +
"SELECT ?c WHERE {{?c a owl:Class} UNION {?c rdfs:subClassOf ?d} UNION {?d rdfs:subClassOf ?c}} LIMIT 1000";
Modified: trunk/components-core/src/main/java/org/dllearner/learningproblems/PosOnlyLP.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/learningproblems/PosOnlyLP.java 2013-01-23 13:30:14 UTC (rev 3890)
+++ trunk/components-core/src/main/java/org/dllearner/learningproblems/PosOnlyLP.java 2013-01-25 12:02:10 UTC (rev 3891)
@@ -64,6 +64,11 @@
public PosOnlyLP(AbstractReasonerComponent reasoningService) {
super(reasoningService);
}
+
+ public PosOnlyLP(AbstractReasonerComponent reasoningService, SortedSet<Individual> positiveExamples) {
+ super(reasoningService);
+ this.positiveExamples = positiveExamples;
+ }
/*
* (non-Javadoc)
Modified: trunk/scripts/pom.xml
===================================================================
--- trunk/scripts/pom.xml 2013-01-23 13:30:14 UTC (rev 3890)
+++ trunk/scripts/pom.xml 2013-01-25 12:02:10 UTC (rev 3891)
@@ -25,6 +25,10 @@
<artifactId>jena</artifactId>
<groupId>com.hp.hpl.jena</groupId>
</exclusion>
+ <exclusion>
+ <artifactId>owlapi</artifactId>
+ <groupId>net.sourceforge.owlapi</groupId>
+ </exclusion>
</exclusions>
</dependency>
<dependency>
@@ -40,6 +44,12 @@
<dependency>
<groupId>org.dllearner</groupId>
<artifactId>interfaces</artifactId>
+ <exclusions>
+ <exclusion>
+ <artifactId>owlapi</artifactId>
+ <groupId>net.sourceforge.owlapi</groupId>
+ </exclusion>
+ </exclusions>
</dependency>
<dependency>
<groupId>net.sourceforge.secondstring</groupId>
@@ -49,12 +59,12 @@
<groupId>postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
- <dependency>
- <groupId>com.dumontierlab</groupId>
- <artifactId>pdb2rdf-parser</artifactId>
- </dependency>
<dependency>
<groupId>com.dumontierlab</groupId>
+ <artifactId>pdb2rdf-parser</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>com.dumontierlab</groupId>
<artifactId>pdb2rdf-cli</artifactId>
<exclusions>
<exclusion>
@@ -84,8 +94,8 @@
<groupId>org.deri.any23</groupId>
</exclusion>
<exclusion>
- <artifactId>jena-core</artifactId>
- <groupId>org.apache.jena</groupId>
+ <artifactId>jena-core</artifactId>
+ <groupId>org.apache.jena</groupId>
</exclusion>
</exclusions>
</dependency>
@@ -103,6 +113,30 @@
<artifactId>weka</artifactId>
<version>3.6.5</version>
</dependency>
+ <dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-distribution</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-reasoner</artifactId>
+ <exclusions>
+ <exclusion>
+ <artifactId>owlapi-api</artifactId>
+ <groupId>net.sourceforge.owlapi</groupId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+ <dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-util</artifactId>
+ <exclusions>
+ <exclusion>
+ <artifactId>owlapi-api</artifactId>
+ <groupId>net.sourceforge.owlapi</groupId>
+ </exclusion>
+ </exclusions>
+ </dependency>
</dependencies>
Added: trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMatching.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMatching.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMatching.java 2013-01-25 12:02:10 UTC (rev 3891)
@@ -0,0 +1,291 @@
+package org.dllearner.scripts;
+
+import java.net.URL;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.core.AbstractLearningProblem;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.ExtractionDBCache;
+import org.dllearner.kb.sparql.SPARQLTasks;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.learningproblems.PosOnlyLP;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.dllearner.utilities.datastructures.Datastructures;
+import org.dllearner.utilities.datastructures.SortedSetTuple;
+import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2;
+
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.Syntax;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
+import com.hp.hpl.jena.vocabulary.OWL;
+import com.jamonapi.Monitor;
+import com.jamonapi.MonitorFactory;
+
+public class OntologyMatching {
+
+
+ private static final Logger logger = Logger.getLogger(OntologyMatching.class.getName());
+
+ private final ObjectProperty sameAs = new ObjectProperty(OWL.sameAs.getURI());
+ private final Monitor mon;
+
+ //KB1
+ private KnowledgeBase kb1;
+ //KB2
+ private KnowledgeBase kb2;
+
+ public OntologyMatching(KnowledgeBase kb1, KnowledgeBase kb2) {
+ this.kb1 = kb1;
+ this.kb2 = kb2;
+
+ mon = MonitorFactory.getTimeMonitor("time");
+ }
+
+ public OntologyMatching(SparqlEndpoint endpoint1, SparqlEndpoint endpoint2) {
+ this(new KnowledgeBase(endpoint1), new KnowledgeBase(endpoint2));
+ }
+
+ public void start(){
+ computeMatching(kb1, kb2);
+ computeMatching(kb2, kb1);
+ }
+
+ private void computeMatching(KnowledgeBase source, KnowledgeBase target) {
+ // get all classes in SOURCE
+ Set<NamedClass> sourceClasses = getClasses(source);
+
+ // for each class of KB1
+ for (NamedClass nc : sourceClasses) {
+ logger.info(nc);
+ // get all via owl:sameAs related individuals
+ SortedSet<Individual> individuals = getRelatedIndividualsNamespaceAware(source, nc, target.getNamespace());
+ logger.info(individuals);
+ //learn concept in KB2 based on the examples
+ if(individuals.size() >= 3){
+ learnClassExpression(target, individuals);
+ }
+ }
+ }
+
+ private void learnClassExpression(KnowledgeBase kb, SortedSet<Individual> posExamples){
+ learnClassExpression(kb, posExamples, false);
+ }
+
+ private void learnClassExpression(KnowledgeBase kb, SortedSet<Individual> positiveExamples, boolean posNeg){
+ try {
+ SortedSet<Individual> negativeExamples = new TreeSet<Individual>();
+ if(posNeg){
+ //find negative examples
+ mon.start();
+ AutomaticNegativeExampleFinderSPARQL2 finder = new AutomaticNegativeExampleFinderSPARQL2(kb.getEndpoint());
+ //TODO find negative examples
+ mon.stop();
+ logger.info("Found " + negativeExamples.size() + " negative examples in " + mon.getLastValue() + "ms.");
+ }
+
+ SortedSetTuple<Individual> examples = new SortedSetTuple<Individual>(positiveExamples, negativeExamples);
+
+ SparqlKnowledgeSource ks = new SparqlKnowledgeSource();
+ ks.setInstances(Datastructures.individualSetToStringSet(examples.getCompleteSet()));
+ ks.setUrl(kb.getEndpoint().getURL());
+ ks.setDefaultGraphURIs(new TreeSet<String>(kb.getEndpoint().getDefaultGraphURIs()));
+ ks.setUseLits(false);
+ ks.setUseCacheDatabase(true);
+ ks.setCacheDir("cache");
+ ks.setRecursionDepth(2);
+ ks.setCloseAfterRecursion(true);
+ ks.setDissolveBlankNodes(false);
+ ks.setSaveExtractedFragment(false);
+ ks.init();
+
+ AbstractReasonerComponent rc = new FastInstanceChecker(ks);
+ rc.init();
+
+ AbstractLearningProblem lp;
+ if(posNeg){
+ lp = new PosNegLPStandard(rc, positiveExamples, negativeExamples);
+ } else {
+ lp = new PosOnlyLP(rc, positiveExamples);
+
+ }
+ lp.init();
+
+ CELOE la = new CELOE(lp, rc);
+ la.setMaxExecutionTimeInSeconds(10);
+ la.setNoisePercentage(25);
+ la.init();
+ la.start();
+
+ logger.info(la.getCurrentlyBestEvaluatedDescription());
+ } catch (ComponentInitException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private Set<NamedClass> getClasses(KnowledgeBase kb){
+ Set<NamedClass> classes = kb.getSparqlHelper().getAllClasses();
+ //fallback: check for ?s a ?type where ?type is not asserted to owl:Class
+ if(classes.isEmpty()){
+ String query = "SELECT ?type WHERE {?s a ?type.}";
+ ResultSet rs = executeSelect(kb, query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ if(qs.get("type").isURIResource()){
+ classes.add(new NamedClass(qs.get("type").asResource().getURI()));
+ }
+ }
+ }
+ return classes;
+ }
+
+ private SortedSet<Individual> getRelatedIndividualsNaive(KnowledgeBase kb, NamedClass nc){
+ SortedSet<Individual> relatedIndividuals = new TreeSet<Individual>();
+ //get all individuals in given class nc
+ Set<Individual> individuals = kb.getReasoner().getIndividuals(nc);
+ //for each individual in class nc
+ for(Individual ind : individuals){
+ //get all individuals related via owl:sameAs
+ Set<Individual> sameIndividuals = kb.getReasoner().getRelatedIndividuals(ind, sameAs);
+ relatedIndividuals.addAll(sameIndividuals);
+ }
+ return relatedIndividuals;
+ }
+
+ private SortedSet<Individual> getRelatedIndividuals(KnowledgeBase kb, NamedClass nc){
+ SortedSet<Individual> relatedIndividuals = new TreeSet<Individual>();
+ //get all individuals o which are connected to individuals s belonging to class nc
+ String query = String.format("SELECT ?o WHERE {?s a <%s>. ?s <http://www.w3.org/2002/07/owl#sameAs> ?o.}", nc.getName());
+ ResultSet rs = executeSelect(kb, query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ RDFNode object = qs.get("o");
+ if(object.isURIResource()){
+ relatedIndividuals.add(new Individual(object.asResource().getURI()));
+ }
+ }
+ return relatedIndividuals;
+ }
+
+ private SortedSet<Individual> getRelatedIndividualsNamespaceAware(KnowledgeBase kb, NamedClass nc, String targetNamespace){
+ SortedSet<Individual> relatedIndividuals = new TreeSet<Individual>();
+ //get all individuals o which are connected to individuals s belonging to class nc
+ String query = String.format("SELECT ?o WHERE {?s a <%s>. ?s <http://www.w3.org/2002/07/owl#sameAs> ?o. FILTER(REGEX(STR(?o),'%s'))}", nc.getName(), targetNamespace);
+ ResultSet rs = executeSelect(kb, query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ RDFNode object = qs.get("o");
+ if(object.isURIResource()){
+ relatedIndividuals.add(new Individual(object.asResource().getURI()));
+ }
+ }
+ return relatedIndividuals;
+ }
+
+ protected ResultSet executeSelect(KnowledgeBase kb, String query){
+ return executeSelect(kb, QueryFactory.create(query, Syntax.syntaxARQ));
+ }
+
+ protected ResultSet executeSelect(KnowledgeBase kb, Query query){
+ ExtractionDBCache cache = kb.getCache();
+ SparqlEndpoint endpoint = kb.getEndpoint();
+ ResultSet rs = null;
+ if(cache != null){
+ rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query.toString()));
+ } else {
+ QueryEngineHTTP qe = new QueryEngineHTTP(endpoint.getURL().toString(), query);
+ for(String uri : endpoint.getDefaultGraphURIs()){
+ qe.addDefaultGraph(uri);
+ }
+ rs = qe.execSelect();
+ }
+ return rs;
+ }
+
+ public static class KnowledgeBase{
+ private SparqlEndpoint endpoint;
+ private SPARQLReasoner reasoner;
+ private SPARQLTasks sparqlHelper;
+ private String namespace;
+ private ExtractionDBCache cache;
+
+ public KnowledgeBase(SparqlEndpoint endpoint, ExtractionDBCache cache, String namespace) {
+ this.endpoint = endpoint;
+ this.namespace = namespace;
+ this.cache = cache;
+
+ this.reasoner = new SPARQLReasoner(new SparqlEndpointKS(endpoint));
+ this.sparqlHelper = new SPARQLTasks(endpoint);
+ }
+
+ public KnowledgeBase(SparqlEndpoint endpoint) {
+ this.endpoint = endpoint;
+
+ this.reasoner = new SPARQLReasoner(new SparqlEndpointKS(endpoint));
+ this.sparqlHelper = new SPARQLTasks(endpoint);
+ }
+
+ public SparqlEndpoint getEndpoint() {
+ return endpoint;
+ }
+
+ public SPARQLReasoner getReasoner() {
+ return reasoner;
+ }
+
+ public SPARQLTasks getSparqlHelper() {
+ return sparqlHelper;
+ }
+
+ public String getNamespace() {
+ return namespace;
+ }
+
+ public ExtractionDBCache getCache() {
+ return cache;
+ }
+
+
+
+ }
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) throws Exception{
+ // KB2
+ SparqlEndpoint endpoint1 = SparqlEndpoint.getEndpointDBpedia();
+ ExtractionDBCache cache1 = new ExtractionDBCache("cache");
+ String namespace1 = "http://dbpedia.org/resource/";
+ KnowledgeBase kb1 = new KnowledgeBase(endpoint1, cache1, namespace1);
+ // KB2
+ SparqlEndpoint endpoint2 = new SparqlEndpoint(new URL("http://wifo5-03.informatik.uni-mannheim.de/factbook/sparql"));
+ ExtractionDBCache cache2 = new ExtractionDBCache("cache");
+ String namespace2 = "http://www4.wiwiss.fu-berlin.de/factbook/resource/";
+ KnowledgeBase kb2 = new KnowledgeBase(endpoint2, cache2, namespace2);
+
+ OntologyMatching matcher = new OntologyMatching(kb1, kb2);
+ matcher.start();
+
+ }
+
+}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/matching/GeneralMatcher.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/matching/GeneralMatcher.java 2013-01-23 13:30:14 UTC (rev 3890)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/matching/GeneralMatcher.java 2013-01-25 12:02:10 UTC (rev 3891)
@@ -24,7 +24,7 @@
import java.util.LinkedList;
import java.util.Set;
-import org.dllearner.algorithm.qtl.QTL;
+import org.dllearner.algorithms.qtl.QTL;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.LearningProblemUnsupportedException;
import org.dllearner.kb.SparqlEndpointKS;
Modified: trunk/test/qtl/dbpedia_simple.conf
===================================================================
--- trunk/test/qtl/dbpedia_simple.conf 2013-01-23 13:30:14 UTC (rev 3890)
+++ trunk/test/qtl/dbpedia_simple.conf 2013-01-25 12:02:10 UTC (rev 3891)
@@ -2,7 +2,7 @@
prefixes = [ ("dbr","http://dbpedia.org/resource/") ]
ks.type = "SPARQL"
-ks.url = "http://live.dbpedia.org/sparql"
+ks.url = "http://dbpedia.org/sparql"
ks.defaultGraphURIs = { "http://dbpedia.org" }
// learning problem
@@ -10,3 +10,4 @@
lp.positiveExamples = { "dbr:Bob_Dylan", "dbr:The_Beatles", "dbr:Aerosmith" }
alg.type = "qtl"
+alg.maxQueryTreeDepth = 1
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